1
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Molina O, Ortega-Sabater C, Thampi N, Fernández-Fuentes N, Guerrero-Murillo M, Martínez-Moreno A, Vinyoles M, Velasco-Hernández T, Bueno C, Trincado JL, Granada I, Campos D, Giménez C, Boer JM, den Boer ML, Calvo GF, Camós M, Fuster JL, Velasco P, Ballerini P, Locatelli F, Mullighan CG, Spierings DCJ, Foijer F, Pérez-García VM, Menéndez P. Chromosomal instability in aneuploid acute lymphoblastic leukemia associates with disease progression. EMBO Mol Med 2024; 16:64-92. [PMID: 38177531 PMCID: PMC10897411 DOI: 10.1038/s44321-023-00006-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Chromosomal instability (CIN) lies at the core of cancer development leading to aneuploidy, chromosomal copy-number heterogeneity (chr-CNH) and ultimately, unfavorable clinical outcomes. Despite its ubiquity in cancer, the presence of CIN in childhood B-cell acute lymphoblastic leukemia (cB-ALL), the most frequent pediatric cancer showing high frequencies of aneuploidy, remains unknown. Here, we elucidate the presence of CIN in aneuploid cB-ALL subtypes using single-cell whole-genome sequencing of primary cB-ALL samples and by generating and functionally characterizing patient-derived xenograft models (cB-ALL-PDX). We report higher rates of CIN across aneuploid than in euploid cB-ALL that strongly correlate with intraclonal chr-CNH and overall survival in mice. This association was further supported by in silico mathematical modeling. Moreover, mass-spectrometry analyses of cB-ALL-PDX revealed a "CIN signature" enriched in mitotic-spindle regulatory pathways, which was confirmed by RNA-sequencing of a large cohort of cB-ALL samples. The link between the presence of CIN in aneuploid cB-ALL and disease progression opens new possibilities for patient stratification and offers a promising new avenue as a therapeutic target in cB-ALL treatment.
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Affiliation(s)
- Oscar Molina
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain.
| | - Carmen Ortega-Sabater
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Namitha Thampi
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Narcís Fernández-Fuentes
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Alba Martínez-Moreno
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Talía Velasco-Hernández
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Juan L Trincado
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Isabel Granada
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Badalona, Spain
- Josep Carreras Leukemia Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | | | | | - Judith M Boer
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L den Boer
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Gabriel F Calvo
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Mireia Camós
- Hematology Laboratory, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumor Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose-Luis Fuster
- Pediatric Hematology and Oncology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Pablo Velasco
- Pediatric Oncology and Hematology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Paola Ballerini
- AP-HP, Service of Pediatric Hematology, Hopital Armand Trousseau, Paris, France
| | - Franco Locatelli
- Bambino Gesù Children's Hospital, Catholic University of Sacred Heart, Rome, Italy
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana C J Spierings
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Víctor M Pérez-García
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Biomedicine. School of Medicine, University of Barcelona, Barcelona, Spain.
- Spanish Cancer Research Network (CIBERONC), ISCIII, Barcelona, Spain.
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2
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Mostovoy Y, Yilmaz F, Chow SK, Chu C, Lin C, Geiger EA, Meeks NJL, Chatfield KC, Coughlin CR, Surti U, Kwok PY, Shaikh TH. Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation. Genetics 2021; 217:6066166. [PMID: 33724415 DOI: 10.1093/genetics/iyaa038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/18/2020] [Indexed: 11/12/2022] Open
Abstract
Segmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. Population-level characterization of SDs has generally been lacking because most techniques used for analyzing these complex regions are both labor and cost intensive. In this study, we have used a high-throughput technique to genotype complex structural variation with a single molecule, long-range optical mapping approach. We characterized SDs and identified novel structural variants (SVs) at 7q11.23, 15q13.3, and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising five super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we localized the microdeletion breakpoints to specific paralogous duplicons located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.
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Affiliation(s)
- Yulia Mostovoy
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Feyza Yilmaz
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA.,Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Catherine Chu
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Chin Lin
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kathryn C Chatfield
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Pediatrics, Section of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA.,Department of Dermatology, UCSF School of Medicine, San Francisco, CA 94143, USA.,Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Pesenti E, Kouprina N, Liskovykh M, Aurich-Costa J, Larionov V, Masumoto H, Earnshaw WC, Molina O. Generation of a Synthetic Human Chromosome with Two Centromeric Domains for Advanced Epigenetic Engineering Studies. ACS Synth Biol 2018; 7:1116-1130. [PMID: 29565577 PMCID: PMC5951608 DOI: 10.1021/acssynbio.8b00018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It is generally accepted that chromatin containing the histone H3 variant CENP-A is an epigenetic mark maintaining centromere identity. However, the pathways leading to the formation and maintenance of centromere chromatin remain poorly characterized due to difficulties of analysis of centromeric repeats in native chromosomes. To address this problem, in our previous studies we generated a human artificial chromosome (HAC) whose centromere contains a synthetic alpha-satellite (alphoid) DNA array containing the tetracycline operator, the alphoidtetO-HAC. The presence of tetO sequences allows the specific targeting of the centromeric region in the HAC with different chromatin modifiers fused to the tetracycline repressor. The alphoidtetO-HAC has been extensively used to investigate protein interactions within the kinetochore and to define the epigenetic signature of centromeric chromatin to maintain a functional kinetochore. In this study, we developed a novel synthetic HAC containing two alphoid DNA arrays with different targeting sequences, tetO, lacO and gal4, the alphoidhybrid-HAC. This new HAC can be used for detailed epigenetic engineering studies because its kinetochore can be simultaneously or independently targeted by different chromatin modifiers and other fusion proteins.
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Affiliation(s)
- Elisa Pesenti
- Wellcome
Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3QR, United
Kingdom
| | - Natalay Kouprina
- Genome
Structure and Function Group, Developmental Therapeutics Branch, National
Cancer Institute, National Institutes of
Health, Bethesda, Maryland 20892, United States
| | - Mikhail Liskovykh
- Genome
Structure and Function Group, Developmental Therapeutics Branch, National
Cancer Institute, National Institutes of
Health, Bethesda, Maryland 20892, United States
| | - Joan Aurich-Costa
- Research
and Development, Cellay Inc., Cambridge, Massachusetts 02139, United States
| | - Vladimir Larionov
- Genome
Structure and Function Group, Developmental Therapeutics Branch, National
Cancer Institute, National Institutes of
Health, Bethesda, Maryland 20892, United States
| | - Hiroshi Masumoto
- Laboratory
of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, Kisazaru 292-0818, Japan
| | - William C. Earnshaw
- Wellcome
Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3QR, United
Kingdom,E-mail: ; tel: +34 93-557-2810
| | - Oscar Molina
- Wellcome
Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3QR, United
Kingdom,Josep
Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain,E-mail: ; tel: +44-(0)131-650-7101
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4
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An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Sci Rep 2017; 7:40031. [PMID: 28059126 PMCID: PMC5216377 DOI: 10.1038/srep40031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/01/2016] [Indexed: 12/13/2022] Open
Abstract
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls. The total number of L9 and K3 copies was also characterized using droplet digital PCR (ddPCR). Although we were unable to confirm variations, we detected an additional L9 amplicon corresponding to a pseudogene. Moreover, none of the eight DGS/VCFS parents-of-origin was heterozygote for the inv(22)(q11.2) haplotype. PRDM9 sequencing showed equivalent allelic distributions between DGS/VCFS parents-of-origin and controls, although a new PRDM9 allele (L50) was identified in one case. Our results support the hypothesis that LCR22s variations influences 22q11.2 NAHR events, however further studies are needed to confirm this association and clarify the contribution of pseudogenes and rare PDRM9 alleles to NAHR susceptibility.
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5
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Booth DG, Beckett AJ, Molina O, Samejima I, Masumoto H, Kouprina N, Larionov V, Prior IA, Earnshaw WC. 3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin. Mol Cell 2016; 64:790-802. [PMID: 27840028 PMCID: PMC5128728 DOI: 10.1016/j.molcel.2016.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/24/2016] [Accepted: 10/05/2016] [Indexed: 11/20/2022]
Abstract
Recent studies have revealed the importance of Ki-67 and the chromosome periphery in chromosome structure and segregation, but little is known about this elusive chromosome compartment. Here we used correlative light and serial block-face scanning electron microscopy, which we term 3D-CLEM, to model the entire mitotic chromosome complement at ultra-structural resolution. Prophase chromosomes exhibit a highly irregular surface appearance with a volume smaller than metaphase chromosomes. This may be because of the absence of the periphery, which associates with chromosomes only after nucleolar disassembly later in prophase. Indeed, the nucleolar volume almost entirely accounts for the extra volume found in metaphase chromosomes. Analysis of wild-type and Ki-67-depleted chromosomes reveals that the periphery comprises 30%–47% of the entire chromosome volume and more than 33% of the protein mass of isolated mitotic chromosomes determined by quantitative proteomics. Thus, chromatin makes up a surprisingly small percentage of the total mass of metaphase chromosomes. 3D-CLEM combines light and serial block-face scanning electron microscopy The complete architecture of all 46 human chromosomes has been defined A large portion of mitotic chromosomes is not composed of chromatin Chromosome volumes determined by light and electron microscopy differ dramatically
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Affiliation(s)
- Daniel G Booth
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK.
| | - Alison J Beckett
- Biomedical Electron Microscopy Unit, Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, L69 3BX Liverpool, UK
| | - Oscar Molina
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Itaru Samejima
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Hiroshi Masumoto
- Department of Frontier Research, Laboratory of Cell Engineering, Kazusa DNA Research Institute, Kisarazu, 292-0818 Chiba, Japan
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
| | - Ian A Prior
- Biomedical Electron Microscopy Unit, Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, L69 3BX Liverpool, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK.
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6
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Guo X, Delio M, Haque N, Castellanos R, Hestand MS, Vermeesch JR, Morrow BE, Zheng D. Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis. Hum Mol Genet 2016; 25:3754-3767. [PMID: 27436579 DOI: 10.1093/hmg/ddw221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 11/13/2022] Open
Abstract
Velo-cardio-facial syndrome/DiGeorge syndrome/22q11.2 deletion syndrome (22q11.2DS) is caused by meiotic non-allelic homologous recombination events between flanking low copy repeats termed LCR22A and LCR22D, resulting in a 3 million base pair (Mb) deletion. Due to their complex structure, large size and high sequence identity, genetic variation within LCR22s among different individuals has not been well characterized. In this study, we sequenced 13 BAC clones derived from LCR22A/D and aligned them with 15 previously available BAC sequences to create a new genetic variation map. The thousands of variants identified by this analysis were not uniformly distributed in the two LCR22s. Moreover, shared single nucleotide variants between LCR22A and LCR22D were enriched in the Breakpoint Cluster Region pseudogene (BCRP) block, suggesting the existence of a possible recombination hotspot there. Interestingly, breakpoints for atypical 22q11.2 rearrangements have previously been located to BCRPs To further explore this finding, we carried out in-depth analyses of whole genome sequence (WGS) data from two unrelated probands harbouring a de novo 3Mb 22q11.2 deletion and their normal parents. By focusing primarily on WGS reads uniquely mapped to LCR22A, using the variation map from our BAC analysis to help resolve allele ambiguity, and by performing PCR analysis, we infer that the deletion breakpoints were most likely located near or within the BCRP module. In summary, we found a high degree of sequence variation in LCR22A and LCR22D and a potential recombination breakpoint near or within the BCRP block, providing a starting point for future breakpoint mapping using additional trios.
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Affiliation(s)
| | | | | | | | | | | | | | - Deyou Zheng
- Department of Neurology .,Department of Genetics.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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7
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS NANO 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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8
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Vergés L, Molina O, Geán E, Vidal F, Blanco J. Deletions and duplications of the 22q11.2 region in spermatozoa from DiGeorge/velocardiofacial fathers. Mol Cytogenet 2014; 7:86. [PMID: 25435913 PMCID: PMC4247602 DOI: 10.1186/s13039-014-0086-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/04/2014] [Indexed: 11/12/2022] Open
Abstract
Background DiGeorge/velocardiofacial syndrome (DGS/VCFS) is the most common deletion syndrome in humans. Low copy repeats flanking the 22q11.2 region confer a substrate for non-allelic homologous recombination (NAHR) events leading to rearrangements. This study sought to identify DGS/VCFS fathers with increased susceptibility to deletions and duplications at the 22q11.2 region in spermatozoa and to assess the particular contribution of intra-chromatid and/or inter-chromatid NAHR. Semen samples from nine DGS/VCFS fathers were analyzed by triple-color FISH using a probe combination that discriminated between normal, deleted and duplicated genotypes. Microsatellite analysis were performed in the parents and the affected children to determine the parental origin of the deleted chromosome 22. Results A significant increase in 22q11.2 deletions was observed in the sperm of two out of nine DGS/VCFS fathers (odds ratio 2.03-fold, P < 0.01), and in both cases the deletion in the offspring was transmitted by the father. Patients with significant increases in sperm anomalies presented a disturbed deletion:duplication 1:1 ratio (P < 0.01). Conclusions Altogether, results support that intra-chromatid NAHR is the mechanism responsible for the higher rate of sperm deletions, which is directly related to the transmission of the deleted chromosome 22 to offspring. Accordingly, the screening of sperm anomalies in the 22q11.2 region should be taken into account in the genetic counseling of DGS/VCFS families.
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Affiliation(s)
- Laia Vergés
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Oscar Molina
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain ; Current address: Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland United Kingdom
| | - Esther Geán
- Secció de Genètica Clínica. Hospital Universitari Sant Joan de Déu, 08950-Esplugues de Llobregat, Barcelona, Spain
| | - Francesca Vidal
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Joan Blanco
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
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9
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Kour G, Kaul S, Dhar MK. Molecular characterization of repetitive DNA sequences from B chromosome in Plantago lagopus L. Cytogenet Genome Res 2013; 142:121-8. [PMID: 24296743 DOI: 10.1159/000356472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2013] [Indexed: 11/19/2022] Open
Abstract
In Plantagolagopus the B chromosome has been reported by our laboratory to be the result of massive amplification of ribosomal DNA sequences. However, the presence of transposable elements and other repetitive DNA sequences together with rDNA could not be ruled out. The present study clearly demonstrated the presence of transposable elements in the B chromosomes. These transposable elements were characterized and their nature assessed. Physical mapping using double fluorescent in situ hybridization was performed using DNA probes for 5S and copia elements. The results clearly proved that the B chromosome is a mix of 5S, 45S rDNA and transposable elements. Based on the FISH and Fiber-FISH patterns, it can be concluded that while 45S rDNA sequences are restricted to the subtelomeric regions, the 5S rDNA sequences are interspersed with transposons in the body of the B chromosome. These results have further enhanced our understanding of the organization and evolution of B chromosomes.
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Affiliation(s)
- G Kour
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
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